Multiutil: 0 transactions from RPC1 have been replayed into the MASTR database
Multiutil: 1 transactions from site RPC1 for the MASTR database were
skipped because they have already been replayed.
Multiutil: CRMMS0054E Caught an exception. Detailed exception information is:
Database registry file "/opt/rational/RationalSDLC/clearquest/CQDB_rgys/cqdb_registry/7.0.0/CQMS.VISA_CQMS.RPC2/DBNAME" does not exist

I find the problem. The account we used to run the import command doesn't have the permissions to write to "/opt/rational/RationalSDLC/clearquest/CQDB_rgys/cqdb_registry/7.0.0/CQMS.VISA_CQMS.RPC2 directory.

I believe running the import command with proper permission after getting new user DB from DBA should solve the issue.